A Phylogenomic and Molecular Markers Based Analysis of the Class Acidimicrobiia

Microcystis genotypes in a tropical freshwater lake: Discovery of novel MIB-producing Microcystis with potentially unique synthesis pathway

Harmful algal blooms (HABs) are a threat to freshwater systems over the world due to the production of hepatotoxins like microcystin (MC), and nuisance taste and odour (T&O) compounds like 2-methylisoborneol (MIB). While MCs are known to cause detrimental effects to both water quality and human health, MIB is only reported to cause aesthetical problems. In this study, we investigated a tropical, urban lake that was experiencing persistent MC and MIB events. Although it was dominated by Microcystis blooms, analysis revealed that the toxigenic Microcystis were not the only species driving the MC concentrations. Additionally, there was also a lack of causative species for the MIB events. Through isolation, we have identified three toxigenic Microcystis found to produce four different variants of MCs, and two novel non-toxigenic Microcystis that were capable of producing MIB. The ability to produce MIB had never been previously reported for this species. Compared to other major producers such as Planktothricoides sp. and Streptomyces sp., the MIB synthase genes of our Microcystis sp. strains were partial, illustrating the possibility of unique synthesis pathways. The Microcystis sp. strains were found to produce about 2.77-5.22 fg MIB cell-1, with a majority of the contents (70-80 %) existing in the extracellular phase. Correlation analysis of field study indicated that phosphorus limitation may have an indirect effect on non-toxigenic Microcystis abundance and proportion by influencing the toxigenic genotype, suggesting that current measures to control HABs may favour the proliferation of the non-toxigenic Microcystis. The potential for Microcystis sp. to produce MIB through unique synthesis pathway, coupled with the potential dominance of non-toxigenic genotypes in Microcystis blooms, signals the possibility that non-toxigenic Microcystis should be monitored as well.

The First Description of the Microbial Diversity in the Amarillo River (La Rioja, Argentina), a Natural Extreme Environment Where the Whole Microbial Community Paints the Landscape Yellow

The Amarillo River in Famatina, La Rioja, Argentina, is a natural acidic river with distinctive yellow-ochreous iron precipitates along its course. While mining activities have occurred in the area, the river's natural acidity is influenced by environmental factors beyond mineralogy, where microbial species have a crucial role. Although iron-oxidising bacteria have been identified, a comprehensive analysis of the entire microbial community in this extreme environment has not yet been conducted. In this study, we employ high-throughput sequencing to explore the bacterial and fungal diversity in the Amarillo River and Cueva de Pérez terraces, considered prehistoric analogues of the current river basin. Fe(II)-enrichment cultures mimicking different environmental conditions of the river were also analysed to better understand the roles of prokaryotes and fungi in iron oxidation processes. Additionally, we investigate the ecological relationships between bacteria and fungi using co-occurrence and network analysis. Our findings reveal a diverse bacterial community in the river and terraces, including uncultured species affiliated with Acidimicrobiia, part of an uncharacterised universal microbial acidic diversity. Acidophiles such as Acidithiobacillus ferrivorans, the main iron oxidiser of the system, and Acidiphilium, which is unable to catalyse Fe(II) oxidation but has a great metabolic flexibility,, are part of the core of the microbial community, showing significant involvement in intraspecies interactions. Alicyclobacillus, which is the main Fe(II) oxidiser in the enrichment culture at 30 °C and is detected all over the system, highlights its flexibility towards the iron cycle. The prevalence of key microorganisms in both rivers and terraces implies their enduring contribution to the iron cycle as well as in shaping the iconic yellow landscape of the Amarillo River. In conclusion, this study enhances our understanding of microbial involvement in iron mineral precipitation, emphasising the collaborative efforts of bacteria and fungi as fundamental geological agents in the Amarillo River.

Bacterial community and culturable actinomycetes of Phyllostachys viridiglaucescens rhizosphere

During the course of development plants form tight interactions with microorganisms inhabiting their root zone. In turn, rhizosphere bacteria, in particular members of the phylum Actinomycetota, positively influence the host plant by increasing access to essential nutrients and controlling the pathogenic microorganism's population. Herein, we report the characterisation of the rhizosphere associated actinobacteria community of Phyllostachys viridiglaucescens growing in the Nikitsky Botanical Garden (Crimean Peninsula, Ukraine). The overall composition of the bacterial community was elucidated by 16S rRNA gene amplicon sequencing followed by isolation of culturable microorganisms with the focus on actinomycetes. The metagenomic approach revealed that the representatives of phylum Actinomycetota (57.1%), Pseudomonadota (20.0%), and Acidobacteriota (12.2%) were dominating in the studied microbiome with Ilumatobacter (phylum Actinomycetota) (13.1%) being the dominant genus. Furthermore, a total of 159 actinomycete isolates, belonging to eight genera of Streptomyces, Micromonospora, Nonomuraea, Arthrobacter, Actinomadura, Kribbella, Cellulosimicrobium, and Mumia, were recovered from P. viridiglaucescens rhizosphere. The isolated species were tested for antimicrobial activity. 64% of isolates were active against at least one bacterial test-culture and 7.5% against fungal test culture. In overall, the rhizosphere bacterial communities act as a great source of actinobacterial diversity with the high potential for production of new bioactive compounds.

High wax ester and triacylglycerol biosynthesis potential in coastal sediments of Antarctic and Subantarctic environments

The wax ester (WE) and triacylglycerol (TAG) biosynthetic potential of marine microorganisms is poorly understood at the microbial community level. The goal of this work was to uncover the prevalence and diversity of bacteria with the potential to synthesize these neutral lipids in coastal sediments of two high latitude environments, and to characterize the gene clusters related to this process. Homolog sequences of the key enzyme, the wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) were retrieved from 13 metagenomes, including subtidal and intertidal sediments of a Subantarctic environment (Ushuaia Bay, Argentina), and subtidal sediments of an Antarctic environment (Potter Cove, Antarctica). The abundance of WS/DGAT homolog sequences in the sediment metagenomes was 1.23 ± 0.42 times the abundance of 12 single-copy genes encoding ribosomal proteins, higher than in seawater (0.13 ± 0.31 times in 338 metagenomes). Homolog sequences were highly diverse, and were assigned to the Pseudomonadota, Actinomycetota, Bacteroidota and Acidobacteriota phyla. The genomic context of WS/DGAT homologs included sequences related to WE and TAG biosynthesis pathways, as well as to other related pathways such as fatty-acid metabolism, suggesting carbon recycling might drive the flux to neutral lipid synthesis. These results indicate the presence of abundant and taxonomically diverse bacterial populations with the potential to synthesize lipid storage compounds in marine sediments, relating this metabolic process to bacterial survival.

DNA Metabarcoding Reveals Cryptic Diversity in Forest Soils on the Isolated Brazilian Trindade Island, South Atlantic

Located 1140 km from the South American coastline in the South Atlantic Ocean and with an age of 4 million years, Trindade Island is the most recent volcanic component of Brazilian territory. Its original native vegetation has been severely damaged by human influence, in particular through the introduction of exotic grazing animals such as goats. However, since the complete eradication of goats and other feral animals in the late 1990s, the island's vegetation has been recovering, and even some endemic species that had been considered extinct have been rediscovered. In this study, we set out to characterize the contemporary cryptic diversity in soils of the recovering native forest of Trindade Island using metabarcoding by high throughput sequencing (HTS). The sequence diversity obtained was dominated by microorganisms, including three domains (Bacteria, Archaea, and Eukarya) and five kingdoms (Fungi, Metazoa, Protozoa, Chromista, and Viridiplantae). Bacteria were represented by 20 phyla and 116 taxa, with Archaea by only one taxon. Fungi were represented by seven phyla and 250 taxa, Viridiplantae by five phyla and six taxa, Protozoa by five phyla and six taxa, Metazoa by three phyla and four taxa and Chromista by two phyla and two taxa. Even after the considerable anthropogenic impacts and devastation of the island's natural forest, our sequence data reveal the presence of a rich and complex diversity of microorganisms, invertebrates, and plants and provide important baseline biodiversity information that will contribute to ecological restoration efforts on the island.

The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga

The island of Hunga Tonga Hunga Ha'apai (HTHH) in the Kingdom of Tonga was formed by Surtseyan eruptions and persisted for 7 years before being obliterated by a massive volcanic eruption on 15 January 2022. Before it was destroyed, HTHH was an unparalleled natural laboratory to study primary succession on a newly formed landmass. We characterized the microbial communities found on the surface sediments of HTHH using a combination of quantitative PCR, marker gene sequencing, and shotgun metagenomic analyses. Contrary to expectations, photosynthetic cyanobacteria were not detected in these sediments, even though they are typically dominant in the earliest stages of primary succession in other terrestrial environments. Instead, our results suggest that the early sediment communities were composed of a diverse array of bacterial taxa, including trace gas oxidizers, anoxygenic photosynthesizers, and chemolithotrophs capable of metabolizing inorganic sulfur, with these bacteria likely sourced from nearby active geothermal environments. While the destruction of HTHH makes it impossible to revisit the site to conduct in situ metabolic measurements or observe how the microbial communities might have continued to change over time, our results do suggest that the early microbial colonizers have unique origins and metabolic capabilities. IMPORTANCE The volcanic island of Hunga Tonga Hunga Ha'apai in the Kingdom of Tonga represents a very rare example of new island formation and thus a unique opportunity to study how organisms colonize a new landmass. We found that the island was colonized by diverse microbial communities shortly after its formation in 2015, with these microbes likely originating from nearby geothermal environments. Primary succession in this system was distinct from that typically observed in other terrestrial environments, with the early microbial colonizers relying on unique metabolic strategies to survive on the surface of this newly formed island, including the capacity to generate energy via sulfur and trace gas metabolism.

Joint role of land cover types and microbial processing on molecular composition of dissolved organic matter in inland lakes

Anthropogenic activities have greatly changed the land use and land cover (LULC) and further influenced the chemical properties and amount of DOM transported into aquatic systems, meanwhile, microbial processing is also critical to DOM molecular composition in freshwaters. However, how they jointly shape DOM's chemical composition and chemodiversity in lakes is poorly understood. Here we examined DOM characteristics for seven inland lakes with three different land cover conditions (forest-dominated, cropland-dominated, and urban-dominated). Results indicated that DOM in cropland-dominated and forest-dominated lakes exhibited more characteristics of terrestrial organic matter, while urban-dominated lakes had more allochthonous organic matter driven by relatively high nutrient input. Human activities extended terrestrial DOM input to lakes and intensified the amount of heteroatomic organic molecules containing nitrogen and sulfur in lakes, with cropland contributing more N-containing compounds and urban contributing more S-containing compounds. Differential bacterial community composition appeared in the three types of land cover lakes, while strong co-occurrence/exclusion patterns between specific microbes and molecular formula groups revealed the key DOM metabolism functions of these bacteria. Matrix correlations based on Mantel tests confirmed that watershed landcover status was a dominating factor for DOM sources and molecular composition in mountainous lakes through direct input of terrestrial organic matter, and microbial processing was not the key factor for DOM molecular formula. Our findings help to assess the influence of human activities and microbial processing in the transfer and transformation of DOM in environmental waters.

Microbiome composition of the marine sponge Cliona varians at the Neotropical Southern Caribbean Sea displays a predominant core of Rhizobiales and Nitrosopumilaceae

AIMS

This work aims to characterize the microbial diversity of the encrusting sponge Cliona varians, a pore-forming and coral reef bioeroding marine sponge of emerging spread related to ocean acidification.

METHODS AND RESULTS

We analyzed the microbiome composition by 16S V4 amplicon next-generation sequencing in a community of the bioeroding coral-reef encrusting/excavating marine sponge Cliona varians thriving at the Southern Caribbean Sea. 87.21% and 6.76% of the sequences retrieved were assigned to the domain Bacteria and Archaea. The most predominant operational taxonomic units were classified as members of the order Rhizobiales and family Nitrosopumilaceae, representing members of not yet characterized genera. Features found strictly conserved in the strain/genomic representatives reported in those microbial taxa are nitrogen fixation and transformation.

CONCLUSION

Our results suggest, in accordance with recent results, that these microbiome members and associated functions could be contributing to the biological fitness of the sponge to be able to colonize and bioerode in environments with low access and scarce availability of nitrogen source.

SIGNIFICANCE AND IMPACT OF STUDY

Coral reefs bioresources such as sponge holobionts are intriguing and complex ecosystems units. This study contributes to the knowledge of how C. varians microbiota is composed or shaped, which is crucial to understand its ecological functions.

Soil Microbiome Composition along the Natural Norway Spruce Forest Life Cycle

Stand-replacing disturbances are a key element of the Norway spruce (Picea abies) forest life cycle. While the effect of a natural disturbance regime on forest physiognomy, spatial structure and pedocomplexity was well described in the literature, its impact on the microbiome, a crucial soil component that mediates nutrient cycling and stand productivity, remains largely unknown. For this purpose, we conducted research on a chronosequence of sites representing the post-disturbance development of a primeval Norway spruce forest in the Calimani Mts., Romania. The sites were selected along a gradient of duration from 16 to 160 years that ranges from ecosystem regeneration phases of recently disturbed open gaps to old-growth forest stands. Based on DNA amplicon sequencing, we followed bacterial and fungal community composition separately in organic, upper mineral and spodic horizons of present Podzol soils. We observed that the canopy opening and subsequent expansion of the grass-dominated understorey increased soil N availability and soil pH, which was reflected in enlarged bacterial abundance and diversity, namely due to the contribution of copiotrophic bacteria that prefer nutrient-richer conditions. The fungal community composition was affected by the disturbance as well but, contrary to our expectations, with no obvious effect on the relative abundance of ectomycorrhizal fungi. Once the mature stand was re-established, the N availability was reduced, the pH gradually decreased and the original old-growth forest microbial community dominated by acidotolerant oligotrophs recovered. The effect of the disturbance and forest regeneration was most evident in organic horizons, while the manifestation of these events was weaker and delayed in deeper soil horizons.

Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia

Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus, we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus, two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus. We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminifera, which paves the way for a deeper understanding of their biodiversity, and facilitates future taxonomic and ecological work.

Phylogenomic revision of the family Streptosporangiaceae, reclassification of Desertactinospora gelatinilytica as Spongiactinospora gelatinilytica comb. nov. and a taxonomic home for the genus Sinosporangium in the family Streptosporangiaceae

In recent years, the results of genome-based phylogenetic analyses have contributed to microbial systematics by increasing the availability of sequenced microbial genomes. Therefore, phylogenomic analysis within large taxa in the phylum Actinobacteria has appeared as a useful tool to clarify the taxonomic positions of ambiguous groups. In this study, we provide a revision of the actinobacterial family Streptosporangiaceae using a large collection of genome data and phylogenomics approaches. The phylogenomic analyses included the publicly available genome data of the members of the family Streptosporangiaceae and the state-of-the-art tools are used to infer the taxonomic affiliation of these species within the family. By comparing genome-based and 16S rRNA gene-based trees, as well as pairwise genome comparisons, the recently described genera Spongiactinospora and Desertactinospora are combined in the genus Spongiactinospora. In conclusion, a comprehensive phylogenomic revision of the family Streptosporangiaceae is proposed.

Electrically conductive membranes for anti-biofouling in membrane distillation with two novel operation modes: Capacitor mode and resistor mode

This study evaluated the anti-biofouling efficacy of capacitor mode and resistor mode in membrane distillation (MD). Polytetrafluoroethylene (PTFE) membrane coated with carbon nanotube (CNT) was adopted as the electrically conductive membrane. The biofouling formation on the pre-treatment membrane was systematically analyzed, and the results showed that both operation modes had obvious inhabitation on bacteria, especially the capacitor mode exhibited stronger prevention capability on biomass accumulation than resistor mode. NMDs analysis of microbial communities further revealed that the anti-biofouling effect mainly occurred on the membrane surface, and gram-positive biomarkers which can survive better in external electric field was distinctively found in capacitor mode through LEfSE analysis. Hypothesis was introduced to explain the anti-fouling function of two modes that in the capacitor mode, the competitive electrostatic repulsion of bacteria cells on negative electrode associated by the cell-disruption effect of electro-catalyzed reactive oxygen species (ROS) generation, while the anti-fouling function of resistor mode was a result of temperature increment on membrane surface caused by Joule heating effects. This article attempts to provide an insight of anti-fouling mechanism of electric field applied in MD and to prove the feasibility of above-mentioned operation modes as non-chemical methods for optimization of membrane-based water treatment process.

Revegetation on abandoned salt ponds relieves the seasonal fluctuation of soil microbiomes

Background

Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and soil microorganisms to reduce the salt concentrations is believed to be environmentally-friendly. However, little is known about the change of bacterial community during salt pond restoration in the context of phytoremediation. In the present study, we used 16S metagenomics to compare seasonal changes of bacterial communities between the revegetated and barren salterns at Sicao, Taiwan.

Results

In both saltern types, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes were predominant at the phylum level. In the revegetated salterns, the soil microbiomes displayed high species diversities and underwent a stepwise transition across seasons. In the barren salterns, the soil microbiomes fluctuated greatly, indicating that mangroves tended to stabilize the soil microorganism communities over the succession. Bacteria in the order Halanaerobiaceae and archaea in the family Halobacteriaceae that were adapted to high salinity exclusively occurred in the barren salterns. Among the 441 persistent operational taxonomic units detected in the revegetated salterns, 387 (87.5%) were present as transient species in the barren salterns. Only 32 persistent bacteria were exclusively detected in the revegetated salterns. Possibly, salt-tolerant plants provided shelters for those new colonizers.

Conclusions

The collective data indicate that revegetation tended to stabilize the microbiome across seasons and enriched the microbial diversity in the salterns, especially species of Planctomycetes and Acidobacteria.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5875-y) contains supplementary material, which is available to authorized users.

Identification of Molecular Markers That Are Specific to the Class Thermoleophilia

The class Thermoleophilia is one of the deep-rooting lineages within the Actinobacteria phylum and metagenomic investigation of microbial diversity suggested that species associated with the class Thermoleophilia are abundant in hot spring and soil samples. However, very few species of this class have been cultivated and characterized. Our understanding of the phylogeny and taxonomy of Thermoleophilia is solely based on 16S rRNA sequence analysis of limited cultivable representatives, but no other phenotypic or genotypic characteristics are known that can clearly discriminate members of this class from the other taxonomic units within the kingdom bacteria. This study reports phylogenomic analysis for 12 sequenced members of this class and clearly resolves the interrelationship of not yet cultivated species with reconstructed genomes and known type species. Comparative genome analysis discovered 12 CSIs in different proteins and 32 CSPs that are specific to all species of this class. In addition, a large number of CSIs or CSPs were identified to be unique to certain lineages within this class. This study represents the first and most comprehensive phylogenetic analysis of the class Thermoleophilia, and the identified CSIs and CSPs provide valuable molecular markers for the identification and delineation of species belonging to this class or its subordinate taxa.